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- PDB-3k0y: Crystal structure of Putative TOXIN related protein (YP_001303978... -

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Basic information

Entry
Database: PDB / ID: 3k0y
TitleCrystal structure of Putative TOXIN related protein (YP_001303978.1) from Parabacteroides distasonis ATCC 8503 at 2.16 A resolution
ComponentsPutative TOXIN related protein
KeywordsTOXIN / Putative TOXIN related protein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / unknown function
Function / homology
Function and homology information


NigD-like, C-terminal beta sandwich domain / NigD-like N-terminal OB domain / NigD-like, C-terminal beta sandwich domain / NigD-like, C-terminal domain superfamily / NigD-like N-terminal OB domain / NigD-like C-terminal beta sandwich domain / NigD-like N-terminal OB domain / NigD-like, N-terminal domain superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel ...NigD-like, C-terminal beta sandwich domain / NigD-like N-terminal OB domain / NigD-like, C-terminal beta sandwich domain / NigD-like, C-terminal domain superfamily / NigD-like N-terminal OB domain / NigD-like C-terminal beta sandwich domain / NigD-like N-terminal OB domain / NigD-like, N-terminal domain superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesParabacteroides distasonis ATCC 8503 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.16 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative TOXIN related protein (YP_001303978.1) from Parabacteroides distasonis ATCC 8503 at 2.16 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 25, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative TOXIN related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6153
Polymers25,7861
Non-polymers8292
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.722, 71.722, 102.566
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein Putative TOXIN related protein


Mass: 25785.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides distasonis ATCC 8503 (bacteria)
Strain: ATCC 8503 / DSM 20701 / NCTC 11152 / Gene: BDI_2637 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A6LF92
#2: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT (RESIDUE 26-253) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUE 26-253) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
12.9558.35THE STRUCTURE WAS PHASED BY MAD METHOD AT 2.46 A RESOLUTION AND REFINED AT 2.16 A RESOLUTION AGAINST A DATASET COLLECTED FROM A DIFFERENT CRYSTAL.
2
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.79
Details: 5.0000% polyethylene glycol 3000, 44.0000% polyethylene glycol 400, 0.1M MES pH 5.79, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
,0.911621
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL9-210.97911
SYNCHROTRONSSRL BL11-120.97835,0.97876
,0.91162
Detector
TypeIDDetectorDateDetails
MARMOSAIC 325 mm CCD1CCDJul 31, 2009Flat collimating mirror, toroid focusing mirror
MARMOSAIC 325 mm CCD2CCDFeb 23, 2009Flat mirror (vertical focusing)
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double crystal monochromatorMADMx-ray1
2Single crystal Si(111) bent monochromator (horizontal focusing)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979111
20.978351
30.978761
ReflectionResolution: 2.16→39.559 Å / Num. obs: 16892 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 52.236 Å2 / Rmerge(I) obs: 0.032 / Net I/σ(I): 19.28
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.16-2.240.6881.8946032891,299.5
2.24-2.330.4662.7886230881,299.3
2.33-2.430.3183.6858629861,299.7
2.43-2.560.2414.9943432601,299.6
2.56-2.720.1527.5896830971,299.5
2.72-2.930.08712.6916331571,299.4
2.93-3.220.04820.8909031381,299.6
3.22-3.690.02535.1923331721,299.4
3.69-4.640.01848.7916931521,299.5
4.64-39.5590.01754.9909131561,298.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHARPphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.16→39.559 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.937 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 10.948 / SU ML: 0.129 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.189 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. PEG-400 (2PE) FRAGMENTS FROM THE CRYSTALLIZATION SOLUTION ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.235 853 5.1 %RANDOM
Rwork0.203 ---
obs0.205 16861 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 92.69 Å2 / Biso mean: 50.118 Å2 / Biso min: 24.05 Å2
Baniso -1Baniso -2Baniso -3
1--1.48 Å2-0.74 Å20 Å2
2---1.48 Å20 Å2
3---2.21 Å2
Refinement stepCycle: LAST / Resolution: 2.16→39.559 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1580 0 23 56 1659
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221656
X-RAY DIFFRACTIONr_bond_other_d0.0010.021073
X-RAY DIFFRACTIONr_angle_refined_deg1.5961.942256
X-RAY DIFFRACTIONr_angle_other_deg0.8532627
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5045199
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.01625.36682
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.14815250
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.405154
X-RAY DIFFRACTIONr_chiral_restr0.0980.2243
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211840
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02323
X-RAY DIFFRACTIONr_mcbond_it0.9221.5992
X-RAY DIFFRACTIONr_mcbond_other0.211.5399
X-RAY DIFFRACTIONr_mcangle_it1.67821606
X-RAY DIFFRACTIONr_scbond_it2.2413664
X-RAY DIFFRACTIONr_scangle_it3.5294.5648
LS refinement shellResolution: 2.16→2.216 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 62 -
Rwork0.253 1160 -
all-1222 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 51.45 Å / Origin y: 19.065 Å / Origin z: 5.97 Å
111213212223313233
T0.1886 Å2-0.0875 Å2-0.0951 Å2-0.1817 Å20.0382 Å2--0.0666 Å2
L2.3937 °21.5787 °20.8588 °2-3.7006 °2-0.0071 °2--1.3899 °2
S0.1345 Å °0.072 Å °-0.0036 Å °0.0284 Å °-0.1037 Å °-0.1479 Å °0.1042 Å °0.0812 Å °-0.0309 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A34 - 87
2X-RAY DIFFRACTION1A97 - 234
3X-RAY DIFFRACTION1A248 - 253

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